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- PDB-3gu4: Crystal structure of DAPKQ23V-AMPPNP -

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Basic information

Entry
Database: PDB / ID: 3gu4
TitleCrystal structure of DAPKQ23V-AMPPNP
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / glycine-rich loop mutant / kinase-AMPPNP complex / Alternative splicing / ANK repeat / Apoptosis / ATP-binding / Calmodulin-binding / Cytoplasm / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / regulation of autophagy / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / postsynaptic density / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMcNamara, L.K. / Schavocky, J.S. / Watterson, D.M. / Brunzelle, J.S.
CitationJournal: To be Published
Title: Enzymatic activity and crystallgoraphic analyses of a glycine-rich loop mutant of DAPK
Authors: McNamara, L.K. / Schavocky, J.S. / Watterson, D.M. / Brunzelle, J.S.
History
DepositionMar 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4032
Polymers33,8971
Non-polymers5061
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.883, 62.431, 88.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Death-associated protein kinase 1 / DAP kinase 1


Mass: 33896.566 Da / Num. of mol.: 1 / Fragment: protein kinase domain / Mutation: Q23V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK, DAPK1, death-associated protein kinase 1 / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): top10
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 1.8 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2008 / Details: Be lenses
RadiationMonochromator: single diamond crysal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 57021 / Num. obs: 57021 / % possible obs: 98.84 % / Redundancy: 5.7 % / Biso Wilson estimate: 20.5 Å2 / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5539 / % possible all: 97.33

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JKS

1jks


Resolution: 1.35→29.44 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.891 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21117 2887 5.1 %RANDOM
Rwork0.18392 ---
obs0.1853 54069 98.84 %-
all-54069 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 31 338 2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222573
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9873517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43124.622119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65515472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.871514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021971
X-RAY DIFFRACTIONr_nbd_refined0.2080.21269
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.258
X-RAY DIFFRACTIONr_mcbond_it0.7541.51573
X-RAY DIFFRACTIONr_mcangle_it1.27622538
X-RAY DIFFRACTIONr_scbond_it1.77631106
X-RAY DIFFRACTIONr_scangle_it2.7284.5979
LS refinement shellResolution: 1.35→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 220 -
Rwork0.207 3863 -
obs--97.33 %

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